[med-svn] [canu] branch master updated (84c922b -> 2671871)
Andreas Tille
tille at debian.org
Sat Sep 2 13:54:56 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch master
in repository canu.
from 84c922b releasing package canu version 1.5+dfsg-1
adds 3dbd24e New upstream version 1.6+dfsg
new 25bd8c2 Updated version 1.6+dfsg from 'upstream/1.6+dfsg'
new 63c8db0 New upstream version
new 76265a4 debhelper 10
new 5520d66 Standards-Version: 4.1.0 (no changes needed)
new 2671871 Fix gcc-7 error (violation of format-security)
The 5 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
.github/ISSUE_TEMPLATE.md | 21 +
README.citation | 2 +-
README.md | 8 +-
addCopyrights-BuildData.pl | 1 +
addCopyrights.dat | 1020 ++++++++++++++++++++
addCopyrights.pl | 30 +-
buildRelease.sh | 35 +-
debian/changelog | 11 +
debian/compat | 2 +-
debian/control | 4 +-
debian/patches/external-deps.patch | 6 +-
debian/patches/gcc-7_format-security.patch | 88 ++
debian/patches/series | 1 +
debian/patches/use-debian-mhap-at-runtime.patch | 8 +-
debian/rules | 2 +-
documentation/source/conf.py | 4 +-
documentation/source/faq.rst | 63 +-
documentation/source/index.rst | 2 +-
documentation/source/parameter-reference.rst | 39 +-
documentation/source/quick-start.rst | 271 ++----
documentation/source/tutorial.rst | 103 +-
src/AS_UTL/AS_UTL_fileIO.C | 35 +-
src/AS_UTL/AS_UTL_fileIO.H | 1 +
src/AS_UTL/AS_UTL_reverseComplement.C | 129 +--
src/AS_UTL/AS_UTL_reverseComplement.H | 6 +-
src/AS_UTL/bitPackedFile.C | 11 +-
src/AS_UTL/timeAndSize.C | 92 +-
src/AS_UTL/timeAndSize.H | 11 +-
src/AS_UTL/writeBuffer.H | 6 +-
src/AS_global.C | 6 +
src/Makefile | 21 +-
src/bogart/AS_BAT_AssemblyGraph.C | 5 +-
src/bogart/AS_BAT_BestOverlapGraph.C | 27 +-
src/bogart/AS_BAT_BestOverlapGraph.H | 1 +
src/bogart/AS_BAT_CreateUnitigs.C | 553 +++++++++--
src/bogart/AS_BAT_CreateUnitigs.H | 12 +-
src/bogart/AS_BAT_DropDeadEnds.C | 297 ++++++
...AS_BAT_MergeOrphans.H => AS_BAT_DropDeadEnds.H} | 26 +-
src/bogart/AS_BAT_Instrumentation.C | 345 ++++---
src/bogart/AS_BAT_Logging.C | 6 +-
src/bogart/AS_BAT_Logging.H | 2 +-
src/bogart/AS_BAT_MarkRepeatReads.C | 85 +-
src/bogart/AS_BAT_MarkRepeatReads.H | 30 +-
src/bogart/AS_BAT_MergeOrphans.C | 919 ++++++++----------
src/bogart/AS_BAT_OptimizePositions.C | 508 ++++++++++
src/bogart/AS_BAT_Outputs.C | 17 +-
src/bogart/AS_BAT_OverlapCache.C | 644 ++++++------
src/bogart/AS_BAT_OverlapCache.H | 136 ++-
src/bogart/AS_BAT_PlaceContains.C | 4 +-
src/bogart/AS_BAT_PlaceReadUsingOverlaps.C | 647 ++++++-------
src/bogart/AS_BAT_PlaceReadUsingOverlaps.H | 18 +-
src/bogart/AS_BAT_PromoteToSingleton.C | 2 +
src/bogart/AS_BAT_ReadInfo.C | 12 +-
src/bogart/AS_BAT_ReadInfo.H | 16 +-
src/bogart/AS_BAT_SplitDiscontinuous.C | 4 +-
src/bogart/AS_BAT_TigGraph.C | 110 ++-
src/bogart/AS_BAT_TigVector.C | 6 +-
src/bogart/AS_BAT_TigVector.H | 2 +
src/bogart/AS_BAT_Unitig.C | 251 ++---
src/bogart/AS_BAT_Unitig.H | 111 ++-
src/bogart/AS_BAT_Unitig_PlaceReadUsingEdges.C | 30 +-
src/bogart/bogart.C | 282 +++---
src/bogart/bogart.mk | 2 +
src/canu_version_update.pl | 4 +-
src/falcon_sense/falcon_sense.C | 4 +-
src/falcon_sense/libfalcon/falcon.C | 4 +
src/fastq-utilities/fastqSample.C | 8 +-
src/gfa/alignGFA.C | 671 +++++++++++--
src/gfa/bed.C | 173 ++++
src/gfa/{gfa.H => bed.H} | 68 +-
src/gfa/gfa.C | 62 +-
src/gfa/gfa.H | 4 +
src/main.mk | 3 +-
src/meryl/libmeryl.C | 34 +-
src/minimap/mmapConvert.C | 65 +-
src/overlapBasedTrimming/splitReads-trimBad.C | 11 +-
src/overlapBasedTrimming/splitReads-workUnit.C | 8 +-
src/overlapBasedTrimming/splitReads.C | 15 +-
src/overlapErrorAdjustment/findErrors.H | 2 +-
src/overlapInCore/libedlib/edlib.C | 205 ++--
src/overlapInCore/libedlib/edlib.H | 18 +-
src/overlapInCore/liboverlap/Binomial_Bound.C | 8 +
src/overlapInCore/overlapInCorePartition.C | 2 +
src/pipelines/canu.pl | 350 ++++---
src/pipelines/canu/Configure.pm | 127 ++-
src/pipelines/canu/Consensus.pm | 120 ++-
src/pipelines/canu/CorrectReads.pm | 29 +-
src/pipelines/canu/Defaults.pm | 712 +++++++-------
src/pipelines/canu/Execution.pm | 195 ++--
src/pipelines/canu/Gatekeeper.pm | 150 +--
src/pipelines/canu/Grid_LSF.pm | 2 +-
src/pipelines/canu/Grid_PBSTorque.pm | 22 +-
src/pipelines/canu/Meryl.pm | 16 +-
src/pipelines/canu/Output.pm | 7 +
src/pipelines/canu/OverlapBasedTrimming.pm | 3 +-
src/pipelines/canu/OverlapErrorAdjustment.pm | 46 +-
src/pipelines/canu/OverlapInCore.pm | 21 +-
src/pipelines/canu/OverlapMMap.pm | 127 ++-
src/pipelines/canu/OverlapMhap.pm | 43 +-
src/pipelines/canu/OverlapStore.pm | 214 ++--
src/pipelines/canu/Unitig.pm | 20 +-
src/stores/gatekeeperPartition.C | 77 +-
src/stores/gkStore.C | 16 +-
src/stores/ovStoreBucketizer.C | 2 +
src/stores/ovStoreDump.C | 18 +-
src/stores/ovStoreIndexer.C | 2 +-
src/stores/ovStoreSorter.C | 39 +-
src/stores/ovStoreWriter.C | 10 +-
src/stores/tgStore.C | 8 +-
src/stores/tgTig.C | 6 +-
src/utgcns/libNDFalcon/LICENSE | 36 -
src/utgcns/libNDFalcon/dw.C | 359 -------
src/utgcns/libNDFalcon/dw.H | 161 ---
src/utgcns/libcns/unitigConsensus.C | 752 ++++++++++-----
src/utgcns/libcns/unitigConsensus.H | 7 +-
src/utgcns/libpbutgcns/Alignment.C | 113 ---
src/utgcns/libpbutgcns/Alignment.H | 65 +-
src/utgcns/libpbutgcns/AlnGraphBoost.C | 8 +-
src/utgcns/libpbutgcns/AlnGraphBoost.H | 6 +-
src/utgcns/utgcns.C | 185 ++--
120 files changed, 8123 insertions(+), 4469 deletions(-)
create mode 100644 .github/ISSUE_TEMPLATE.md
create mode 100644 debian/patches/gcc-7_format-security.patch
create mode 100644 src/bogart/AS_BAT_DropDeadEnds.C
copy src/bogart/{AS_BAT_MergeOrphans.H => AS_BAT_DropDeadEnds.H} (70%)
create mode 100644 src/bogart/AS_BAT_OptimizePositions.C
create mode 100644 src/gfa/bed.C
copy src/gfa/{gfa.H => bed.H} (58%)
delete mode 100644 src/utgcns/libNDFalcon/LICENSE
delete mode 100644 src/utgcns/libNDFalcon/dw.C
delete mode 100644 src/utgcns/libNDFalcon/dw.H
delete mode 100644 src/utgcns/libpbutgcns/Alignment.C
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